X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FPCAPanel.java;h=a75de066eaee9a93d56416be9c563a12f32768d0;hb=38299bef6dfd4b713f615781e631dcb66e1155f2;hp=f652aae504245316c29cc2aa225fc00b6b5baa13;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index f652aae..a75de06 100755
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -1,120 +1,153 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
-*/
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 
 package jalview.appletgui;
 
-import jalview.datamodel.*;
-import jalview.analysis.PCA;
-import jalview.jbappletgui.*;
+import java.util.*;
+
 import java.awt.*;
 import java.awt.event.*;
-import java.util.*;
+
+import jalview.analysis.*;
+import jalview.datamodel.*;
 
 
-public class PCAPanel extends GPCAPanel implements Runnable
+public class PCAPanel
+    extends Frame implements Runnable, ActionListener, ItemListener
 {
   PCA pca;
   int top;
   RotatableCanvas rc;
   AlignViewport av;
+  SequenceI [] seqs;
 
-  public void run()
-  {
-    // do stuff
-  }
-
-  public PCAPanel(AlignViewport av, SequenceI[] s) {
 
-    this.av = av;
-    if(av.getSelectionGroup().getSize()>3)
+  public PCAPanel(AlignViewport av)
+  {
+    try
     {
-      s = new Sequence[av.getSelectionGroup().getSize()];
-      for(int i=0; i<s.length; i++)
-        s[i] = av.getSelectionGroup().getSequenceAt(i);
+      jbInit();
     }
-
-
-    if(s==null)
+    catch (Exception e)
     {
-      s = new Sequence[av.getAlignment().getHeight()];
-      for (int i = 0; i < av.getAlignment().getHeight(); i++)
-        s[i] = av.getAlignment().getSequenceAt(i);
-     }
-
-//////////////////////This part was done in PCATHread originally. Is it too slow???
-    pca = new PCA(s);
-    pca.run();
+      e.printStackTrace();
+    }
 
-    // Now find the component coordinates
-    int ii=0;
-    while (ii < s.length && s[ii] != null)
+    for (int i = 1; i < 8; i++)
     {
-      ii++;
+      xCombobox.addItem("dim " + i);
+      yCombobox.addItem("dim " + i);
+      zCombobox.addItem("dim " + i);
     }
 
-    double[][] comps = new double[ii][ii];
-
-    for (int i=0; i < ii; i++ )
+    this.av = av;
+    if (av.getSelectionGroup()!=null && av.getSelectionGroup().getSize() > 3)
     {
-      if (pca.getEigenvalue(i) > 1e-4)
+      seqs = new Sequence[av.getSelectionGroup().getSize()];
+      for (int i = 0; i < av.getSelectionGroup().getSize(); i++)
       {
-        comps[i]  = pca.component(i);
+        seqs[i] = av.getSelectionGroup().getSequenceAt(i);
+      }
+    }
+    else
+    {
+      seqs = new Sequence[av.getAlignment().getHeight()];
+      for (int i = 0; i < av.getAlignment().getHeight(); i++)
+      {
+        seqs[i] = av.getAlignment().getSequenceAt(i);
       }
     }
 
-    //////////////////
+    rc = new RotatableCanvas(av);
+    add(rc, BorderLayout.CENTER);
 
-    xCombobox.select(0);
-    yCombobox.select(1);
-    zCombobox.select(2);
+    jalview.bin.JalviewLite.addFrame(this, "Principal component analysis",
+                                       400, 400);
 
-    top = pca.getM().rows-1;
 
-    Vector points = new Vector();
-    float[][] scores = pca.getComponents(top-1,top-2,top-3,100);
+    Thread worker = new Thread(this);
+    worker.start();
+  }
 
-    for (int i =0; i < pca.getM().rows; i++ )
-    {
-      SequencePoint sp = new SequencePoint(s[i],scores[i]);
-      points.addElement(sp);
-    }
+  /**
+   * DOCUMENT ME!
+   */
+  public void run()
+  {
+              pca = new PCA(seqs);
+              pca.run();
 
-    rc = new RotatableCanvas(av,points,pca.getM().rows);
+              // Now find the component coordinates
+              int ii = 0;
 
-    //rc.printPoints();
+              while ((ii < seqs.length) && (seqs[ii] != null))
+              {
+                  ii++;
+              }
 
-    add(rc, BorderLayout.CENTER);
-  }
+              double[][] comps = new double[ii][ii];
+
+              for (int i = 0; i < ii; i++)
+              {
+                  if (pca.getEigenvalue(i) > 1e-4)
+                  {
+                      comps[i] = pca.component(i);
+                  }
+              }
+
+              //////////////////
+              xCombobox.select(0);
+              yCombobox.select(1);
+              zCombobox.select(2);
 
+              top = pca.getM().rows - 1;
+
+              Vector points = new Vector();
+              float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
+
+              for (int i = 0; i < pca.getM().rows; i++)
+              {
+                  SequencePoint sp = new SequencePoint(seqs[i], scores[i]);
+                  points.addElement(sp);
+              }
+
+              rc.setPoints(points, pca.getM().rows);
+              rc.repaint();
+              seqs = null;
+              this.repaint();
+  }
 
   void doDimensionChange()
   {
-    if(top==0)
+    if (top == 0)
+    {
       return;
+    }
 
     int dim1 = top - xCombobox.getSelectedIndex();
     int dim2 = top - yCombobox.getSelectedIndex();
     int dim3 = top - zCombobox.getSelectedIndex();
 
-    float[][] scores  = pca.getComponents(dim1,dim2,dim3,100);
-    for (int i=0; i < pca.getM().rows; i++) {
-      ((SequencePoint)rc.points.elementAt(i)).coord = scores[i];
+    float[][] scores = pca.getComponents(dim1, dim2, dim3, 100);
+    for (int i = 0; i < pca.getM().rows; i++)
+    {
+      ( (SequencePoint) rc.points.elementAt(i)).coord = scores[i];
     }
 
     rc.img = null;
@@ -123,19 +156,103 @@ public class PCAPanel extends GPCAPanel implements Runnable
     rc.paint(rc.getGraphics());
   }
 
-  protected void xCombobox_actionPerformed(ActionEvent e)
+  public void actionPerformed(ActionEvent evt)
+  {
+    values_actionPerformed();
+  }
+
+  public void itemStateChanged(ItemEvent evt)
+  {
+    if(evt.getSource()==xCombobox)
+      xCombobox_actionPerformed();
+    else if(evt.getSource()==yCombobox)
+      yCombobox_actionPerformed();
+    else if(evt.getSource()==zCombobox)
+      zCombobox_actionPerformed();
+  }
+
+
+  protected void xCombobox_actionPerformed()
   {
     doDimensionChange();
   }
 
-  protected void yCombobox_actionPerformed(ActionEvent e)
+  protected void yCombobox_actionPerformed()
   {
     doDimensionChange();
   }
 
-  protected void zCombobox_actionPerformed(ActionEvent e)
+  protected void zCombobox_actionPerformed()
   {
     doDimensionChange();
   }
 
+  public void values_actionPerformed()
+  {
+
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
+    Frame frame = new Frame();
+    frame.add(cap);
+    jalview.bin.JalviewLite.addFrame(frame, "PCA details", 500, 500);
+
+      cap.setText(pca.getDetails());
+  }
+
+  public void labels_itemStateChanged(ItemEvent itemEvent)
+  {
+    rc.showLabels( labels.getState() );
+  }
+  Panel jPanel2 = new Panel();
+  Label jLabel1 = new Label();
+  Label jLabel2 = new Label();
+  Label jLabel3 = new Label();
+  protected Choice xCombobox = new Choice();
+  protected Choice yCombobox = new Choice();
+  protected Choice zCombobox = new Choice();
+  FlowLayout flowLayout1 = new FlowLayout();
+  BorderLayout borderLayout1 = new BorderLayout();
+  MenuBar menuBar1 = new MenuBar();
+  Menu menu1 = new Menu();
+  Menu menu2 = new Menu();
+  protected CheckboxMenuItem labels = new CheckboxMenuItem();
+  MenuItem values = new MenuItem();
+
+  private void jbInit()
+      throws Exception
+  {
+    this.setLayout(borderLayout1);
+    jPanel2.setLayout(flowLayout1);
+    jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
+    jLabel1.setText("x=");
+    jLabel2.setFont(new java.awt.Font("Verdana", 0, 12));
+    jLabel2.setText("y=");
+    jLabel3.setFont(new java.awt.Font("Verdana", 0, 12));
+    jLabel3.setText("z=");
+    jPanel2.setBackground(Color.white);
+    zCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
+    zCombobox.addItemListener(this);
+    yCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
+    yCombobox.addItemListener(this);
+    xCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
+    xCombobox.addItemListener(this);
+    this.setMenuBar(menuBar1);
+    menu1.setLabel("File");
+    menu2.setLabel("View");
+    labels.setLabel("Labels");
+    labels.addItemListener(this);
+    values.setLabel("Output Values...");
+    values.addActionListener(this);
+    this.add(jPanel2, BorderLayout.SOUTH);
+    jPanel2.add(jLabel1, null);
+    jPanel2.add(xCombobox, null);
+    jPanel2.add(jLabel2, null);
+    jPanel2.add(yCombobox, null);
+    jPanel2.add(jLabel3, null);
+    jPanel2.add(zCombobox, null);
+    menuBar1.add(menu1);
+    menuBar1.add(menu2);
+    menu2.add(labels);
+    menu1.add(values);
+  }
+
 }